Today I spent some more time on the sliding canopy, first off by trimming about 2-3mm off the bottom of the right side to help it sit properly inside the skirt pieces.
After marking the trim line it was out with the Dremel, and, slowly slowly, off with the perspex. It was very cold in the hangar today, so I had a patio heater set up to keep the perspex warm.
After cutting I sanded the edge flat with some 80 grit sandpaper, then smoothed using the edge of a small steel rule as a scraper. This creates a really smooth finish.